Integrative information theoretic network analysis for genome-wide association study of aspirin exacerbated respiratory disease in Korean population View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2017-05-24

AUTHORS

Sehee Wang, Hyun-hwan Jeong, Dokyoon Kim, Kyubum Wee, Hae-Sim Park, Seung-Hyun Kim, Kyung-Ah Sohn

ABSTRACT

BackgroundAspirin Exacerbated Respiratory Disease (AERD) is a chronic medical condition that encompasses asthma, nasal polyposis, and hypersensitivity to aspirin and other non-steroidal anti-inflammatory drugs. Several previous studies have shown that part of the genetic effects of the disease may be induced by the interaction of multiple genetic variants. However, heavy computational cost as well as the complexity of the underlying biological mechanism has prevented a thorough investigation of epistatic interactions and thus most previous studies have typically considered only a small number of genetic variants at a time.MethodsIn this study, we propose a gene network based analysis framework to identify genetic risk factors from a genome-wide association study dataset. We first derive multiple single nucleotide polymorphisms (SNP)-based epistasis networks that consider marginal and epistatic effects by using different information theoretic measures. Each SNP epistasis network is converted into a gene-gene interaction network, and the resulting gene networks are combined as one for downstream analysis. The integrated network is validated on existing knowledgebase of DisGeNET for known gene-disease associations and GeneMANIA for biological function prediction.ResultsWe demonstrated our proposed method on a Korean GWAS dataset, which has genotype information of 440,094 SNPs for 188 cases and 247 controls. The topological properties of the generated networks are examined for scale-freeness, and we further performed various statistical analyses in the Allergy and Asthma Portal (AAP) using the selected genes from our integrated network.ConclusionsOur result reveals that there are several gene modules in the network that are of biological significance and have evidence for controlling susceptibility and being related to the treatment of AERD. More... »

PAGES

31

References to SciGraph publications

  • 2013-08-02. TGFβ — too much of a good thing? in NATURE REVIEWS IMMUNOLOGY
  • 2007-08-26. Bayesian inference of epistatic interactions in case-control studies in NATURE GENETICS
  • 2015-01-08. Performance of genetic programming optimised Bowtie2 on genome comparison and analytic testing (GCAT) benchmarks in BIODATA MINING
  • 2003-04. Pathogenesis of aspirin-exacerbated respiratory disease in CLINICAL REVIEWS IN ALLERGY & IMMUNOLOGY
  • 2014-01-03. New mini- zincin structures provide a minimal scaffold for members of this metallopeptidase superfamily in BMC BIOINFORMATICS
  • 2011-09-12. Characterizing genetic interactions in human disease association studies using statistical epistasis networks in BMC BIOINFORMATICS
  • 2015-06. Characterizing gene-gene interactions in a statistical epistasis network of twelve candidate genes for obesity in BIODATA MINING
  • 2014-04-10. Cloud computing for detecting high-order genome-wide epistatic interaction via dynamic clustering in BMC BIOINFORMATICS
  • 2015-03-27. A targeted analysis identifies a high frequency of BRCA1 and BRCA2 mutation carriers in women with ovarian cancer from a founder population in JOURNAL OF OVARIAN RESEARCH
  • 2003. Analyzing Attribute Dependencies in KNOWLEDGE DISCOVERY IN DATABASES: PKDD 2003
  • 2010-07-08. Surfing a genetic association interaction network to identify modulators of antibody response to smallpox vaccine in GENES & IMMUNITY
  • 2015-07-03. Integrative network analysis for survival-associated gene-gene interactions across multiple genomic profiles in ovarian cancer in JOURNAL OF OVARIAN RESEARCH
  • 2012-11-21. Genome-wide association study of aspirin-exacerbated respiratory disease in a Korean population in HUMAN GENETICS
  • 2012-03-29. Differential gene expression profile in PBMCs from subjects with AERD and ATA: a gene marker for AERD in MOLECULAR GENETICS AND GENOMICS
  • 2008-04-01. Association of Four-locus Gene Interaction with Aspirin-intolerant Asthma in Korean Asthmatics in JOURNAL OF CLINICAL IMMUNOLOGY
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/s12920-017-0266-1

    DOI

    http://dx.doi.org/10.1186/s12920-017-0266-1

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1085588852

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/28589859


    Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
    Incoming Citations Browse incoming citations for this publication using opencitations.net

    JSON-LD is the canonical representation for SciGraph data.

    TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

    [
      {
        "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
        "about": [
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Biological Sciences", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Genetics", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Asthma, Aspirin-Induced", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Epigenesis, Genetic", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Gene Ontology", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Gene Regulatory Networks", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Genome-Wide Association Study", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Humans", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Polymorphism, Single Nucleotide", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Republic of Korea", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Department of Software and Computer Engineering, Ajou University, 16499, Suwon, South Korea", 
              "id": "http://www.grid.ac/institutes/grid.251916.8", 
              "name": [
                "Department of Software and Computer Engineering, Ajou University, 16499, Suwon, South Korea"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Wang", 
            "givenName": "Sehee", 
            "id": "sg:person.011037520407.10", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011037520407.10"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Human and Molecular Genetics, Baylor College of Medicine, 77030, Houston, Texas, USA", 
              "id": "http://www.grid.ac/institutes/grid.39382.33", 
              "name": [
                "Jan and Dan Duncan Neurological Research Institute at Texas Children\u2019s Hospital, 77030, Houston, Texas, USA", 
                "Department of Human and Molecular Genetics, Baylor College of Medicine, 77030, Houston, Texas, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Jeong", 
            "givenName": "Hyun-hwan", 
            "id": "sg:person.0741347305.11", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0741347305.11"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA", 
              "id": "http://www.grid.ac/institutes/grid.29857.31", 
              "name": [
                "Department of Biomedical & Translational Informatics, Geisinger Health System, 17822, Danville, PA, USA", 
                "The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Kim", 
            "givenName": "Dokyoon", 
            "id": "sg:person.01341553516.04", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01341553516.04"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Software and Computer Engineering, Ajou University, 16499, Suwon, South Korea", 
              "id": "http://www.grid.ac/institutes/grid.251916.8", 
              "name": [
                "Department of Software and Computer Engineering, Ajou University, 16499, Suwon, South Korea"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Wee", 
            "givenName": "Kyubum", 
            "id": "sg:person.0745210405.35", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0745210405.35"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Allergy and Clinical Immunology, Ajou University School of Medicine, Suwon, South Korea", 
              "id": "http://www.grid.ac/institutes/grid.251916.8", 
              "name": [
                "Department of Allergy and Clinical Immunology, Ajou University School of Medicine, Suwon, South Korea"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Park", 
            "givenName": "Hae-Sim", 
            "id": "sg:person.010200047735.02", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.010200047735.02"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Translational Research Laboratory for Inflammatory Disease, Clinical Trial Center, Ajou University Medical Center, Suwon, South Korea", 
              "id": "http://www.grid.ac/institutes/grid.411261.1", 
              "name": [
                "Department of Allergy and Clinical Immunology, Ajou University School of Medicine, Suwon, South Korea", 
                "Translational Research Laboratory for Inflammatory Disease, Clinical Trial Center, Ajou University Medical Center, Suwon, South Korea"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Kim", 
            "givenName": "Seung-Hyun", 
            "id": "sg:person.01255615162.64", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01255615162.64"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Software and Computer Engineering, Ajou University, 16499, Suwon, South Korea", 
              "id": "http://www.grid.ac/institutes/grid.251916.8", 
              "name": [
                "Department of Software and Computer Engineering, Ajou University, 16499, Suwon, South Korea"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Sohn", 
            "givenName": "Kyung-Ah", 
            "id": "sg:person.01147724375.97", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01147724375.97"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "sg:pub.10.1038/ng2110", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1008850890", 
              "https://doi.org/10.1038/ng2110"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nri3519", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1010662448", 
              "https://doi.org/10.1038/nri3519"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s13048-015-0171-1", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1045835208", 
              "https://doi.org/10.1186/s13048-015-0171-1"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/978-3-540-39804-2_22", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1029899008", 
              "https://doi.org/10.1007/978-3-540-39804-2_22"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s13040-014-0034-0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1043371184", 
              "https://doi.org/10.1186/s13040-014-0034-0"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s10875-008-9190-7", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1043854554", 
              "https://doi.org/10.1007/s10875-008-9190-7"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00438-012-0685-9", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1048639933", 
              "https://doi.org/10.1007/s00438-012-0685-9"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2105-12-364", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1034115657", 
              "https://doi.org/10.1186/1471-2105-12-364"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/gene.2010.37", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1020223793", 
              "https://doi.org/10.1038/gene.2010.37"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2105-15-1", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1030123122", 
              "https://doi.org/10.1186/1471-2105-15-1"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1385/criai:24:2:169", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1047553932", 
              "https://doi.org/10.1385/criai:24:2:169"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s13048-015-0124-8", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1024213499", 
              "https://doi.org/10.1186/s13048-015-0124-8"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s13040-015-0077-x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1034836750", 
              "https://doi.org/10.1186/s13040-015-0077-x"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00439-012-1247-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1040692595", 
              "https://doi.org/10.1007/s00439-012-1247-2"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2105-15-102", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1045340124", 
              "https://doi.org/10.1186/1471-2105-15-102"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2017-05-24", 
        "datePublishedReg": "2017-05-24", 
        "description": "BackgroundAspirin Exacerbated Respiratory Disease (AERD) is a chronic medical condition that encompasses asthma, nasal polyposis, and hypersensitivity to aspirin and other non-steroidal anti-inflammatory drugs. Several previous studies have shown that part of the genetic effects of the disease may be induced by the interaction of multiple genetic variants. However, heavy computational cost as well as the complexity of the underlying biological mechanism has prevented a thorough investigation of epistatic interactions and thus most previous studies have typically considered only a small number of genetic variants at a time.MethodsIn this study, we propose a gene network based analysis framework to identify genetic risk factors from a genome-wide association study dataset. We first derive multiple single nucleotide polymorphisms (SNP)-based epistasis networks that consider marginal and epistatic effects by using different information theoretic measures. Each SNP epistasis network is converted into a gene-gene interaction network, and the resulting gene networks are combined as one for downstream analysis. The integrated network is validated on existing knowledgebase of DisGeNET for known gene-disease associations and GeneMANIA for biological function prediction.ResultsWe demonstrated our proposed method on a Korean GWAS dataset, which has genotype information of 440,094 SNPs for 188 cases and 247 controls. The topological properties of the generated networks are examined for scale-freeness, and we further performed various statistical analyses in the Allergy and Asthma Portal (AAP) using the selected genes from our integrated network.ConclusionsOur result reveals that there are several gene modules in the network that are of biological significance and have evidence for controlling susceptibility and being related to the treatment of AERD.", 
        "genre": "article", 
        "id": "sg:pub.10.1186/s12920-017-0266-1", 
        "inLanguage": "en", 
        "isAccessibleForFree": true, 
        "isPartOf": [
          {
            "id": "sg:journal.1039191", 
            "issn": [
              "1755-8794"
            ], 
            "name": "BMC Medical Genomics", 
            "publisher": "Springer Nature", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "Suppl 1", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "10"
          }
        ], 
        "keywords": [
          "heavy computational cost", 
          "biological function prediction", 
          "epistasis networks", 
          "information-theoretic measures", 
          "gene networks", 
          "theoretic measures", 
          "computational cost", 
          "integrated network", 
          "genome-wide association study dataset", 
          "network", 
          "genome-wide association studies", 
          "function prediction", 
          "analysis framework", 
          "genetic variants", 
          "gene-disease associations", 
          "gene-gene interaction networks", 
          "dataset", 
          "multiple single nucleotide polymorphisms", 
          "multiple genetic variants", 
          "single nucleotide polymorphisms", 
          "different information theoretic measures", 
          "GWAS datasets", 
          "gene modules", 
          "epistatic interactions", 
          "interaction networks", 
          "epistatic effects", 
          "network analysis", 
          "association studies", 
          "downstream analysis", 
          "biological significance", 
          "genetic effects", 
          "study dataset", 
          "nucleotide polymorphisms", 
          "underlying biological mechanisms", 
          "knowledgebase", 
          "genotype information", 
          "biological mechanisms", 
          "genetic risk factors", 
          "portal", 
          "topological properties", 
          "complexity", 
          "module", 
          "small number", 
          "framework", 
          "information", 
          "previous studies", 
          "genes", 
          "GeneMANIA", 
          "variants", 
          "cost", 
          "SNPs", 
          "ConclusionsOur results", 
          "DisGeNET", 
          "polymorphism", 
          "interaction", 
          "prediction", 
          "method", 
          "Korean population", 
          "thorough investigation", 
          "mechanism", 
          "number", 
          "disease", 
          "analysis", 
          "population", 
          "time", 
          "susceptibility", 
          "part", 
          "results", 
          "study", 
          "control", 
          "evidence", 
          "effect", 
          "statistical analysis", 
          "hypersensitivity", 
          "measures", 
          "factors", 
          "significance", 
          "respiratory disease", 
          "association", 
          "ResultsWe", 
          "cases", 
          "conditions", 
          "polyposis", 
          "AERD", 
          "drugs", 
          "medical conditions", 
          "treatment", 
          "investigation", 
          "properties", 
          "MethodsIn", 
          "asthma", 
          "anti-inflammatory drugs", 
          "allergy", 
          "non-steroidal anti-inflammatory drugs", 
          "nasal polyposis", 
          "risk factors", 
          "aspirin", 
          "chronic medical conditions"
        ], 
        "name": "Integrative information theoretic network analysis for genome-wide association study of aspirin exacerbated respiratory disease in Korean population", 
        "pagination": "31", 
        "productId": [
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1085588852"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1186/s12920-017-0266-1"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "28589859"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1186/s12920-017-0266-1", 
          "https://app.dimensions.ai/details/publication/pub.1085588852"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2022-05-10T10:15", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-springernature-scigraph/baseset/20220509/entities/gbq_results/article/article_742.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://doi.org/10.1186/s12920-017-0266-1"
      }
    ]
     

    Download the RDF metadata as:  json-ld nt turtle xml License info

    HOW TO GET THIS DATA PROGRAMMATICALLY:

    JSON-LD is a popular format for linked data which is fully compatible with JSON.

    curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/s12920-017-0266-1'

    N-Triples is a line-based linked data format ideal for batch operations.

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/s12920-017-0266-1'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/s12920-017-0266-1'

    RDF/XML is a standard XML format for linked data.

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/s12920-017-0266-1'


     

    This table displays all metadata directly associated to this object as RDF triples.

    307 TRIPLES      22 PREDICATES      147 URIs      124 LITERALS      15 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1186/s12920-017-0266-1 schema:about N0ffc99a760e44838b1148913c968f290
    2 N3a15e098ed744efbb0d67099f9127df1
    3 N4d1fc1d071b5467d97915b8a72ce2bb2
    4 N6bd5e09f7ed547149ea3e28c24c647fb
    5 N6e02a263c05547d39c37145e057b932c
    6 Nb378dbd9658448a6b8012e9472ce8f68
    7 Ncef87b20e0ac45739aadd7883b850f7a
    8 Nf43b0ded07b74bd8affcb479d42caf54
    9 anzsrc-for:06
    10 anzsrc-for:0604
    11 schema:author N89284011f1d440ecb1ae1a9de5bc0a05
    12 schema:citation sg:pub.10.1007/978-3-540-39804-2_22
    13 sg:pub.10.1007/s00438-012-0685-9
    14 sg:pub.10.1007/s00439-012-1247-2
    15 sg:pub.10.1007/s10875-008-9190-7
    16 sg:pub.10.1038/gene.2010.37
    17 sg:pub.10.1038/ng2110
    18 sg:pub.10.1038/nri3519
    19 sg:pub.10.1186/1471-2105-12-364
    20 sg:pub.10.1186/1471-2105-15-1
    21 sg:pub.10.1186/1471-2105-15-102
    22 sg:pub.10.1186/s13040-014-0034-0
    23 sg:pub.10.1186/s13040-015-0077-x
    24 sg:pub.10.1186/s13048-015-0124-8
    25 sg:pub.10.1186/s13048-015-0171-1
    26 sg:pub.10.1385/criai:24:2:169
    27 schema:datePublished 2017-05-24
    28 schema:datePublishedReg 2017-05-24
    29 schema:description BackgroundAspirin Exacerbated Respiratory Disease (AERD) is a chronic medical condition that encompasses asthma, nasal polyposis, and hypersensitivity to aspirin and other non-steroidal anti-inflammatory drugs. Several previous studies have shown that part of the genetic effects of the disease may be induced by the interaction of multiple genetic variants. However, heavy computational cost as well as the complexity of the underlying biological mechanism has prevented a thorough investigation of epistatic interactions and thus most previous studies have typically considered only a small number of genetic variants at a time.MethodsIn this study, we propose a gene network based analysis framework to identify genetic risk factors from a genome-wide association study dataset. We first derive multiple single nucleotide polymorphisms (SNP)-based epistasis networks that consider marginal and epistatic effects by using different information theoretic measures. Each SNP epistasis network is converted into a gene-gene interaction network, and the resulting gene networks are combined as one for downstream analysis. The integrated network is validated on existing knowledgebase of DisGeNET for known gene-disease associations and GeneMANIA for biological function prediction.ResultsWe demonstrated our proposed method on a Korean GWAS dataset, which has genotype information of 440,094 SNPs for 188 cases and 247 controls. The topological properties of the generated networks are examined for scale-freeness, and we further performed various statistical analyses in the Allergy and Asthma Portal (AAP) using the selected genes from our integrated network.ConclusionsOur result reveals that there are several gene modules in the network that are of biological significance and have evidence for controlling susceptibility and being related to the treatment of AERD.
    30 schema:genre article
    31 schema:inLanguage en
    32 schema:isAccessibleForFree true
    33 schema:isPartOf N37aac2530dbb4155b25b79433c3b2f6a
    34 N37d0f0bb3420498592a8684cd9d59e20
    35 sg:journal.1039191
    36 schema:keywords AERD
    37 ConclusionsOur results
    38 DisGeNET
    39 GWAS datasets
    40 GeneMANIA
    41 Korean population
    42 MethodsIn
    43 ResultsWe
    44 SNPs
    45 allergy
    46 analysis
    47 analysis framework
    48 anti-inflammatory drugs
    49 aspirin
    50 association
    51 association studies
    52 asthma
    53 biological function prediction
    54 biological mechanisms
    55 biological significance
    56 cases
    57 chronic medical conditions
    58 complexity
    59 computational cost
    60 conditions
    61 control
    62 cost
    63 dataset
    64 different information theoretic measures
    65 disease
    66 downstream analysis
    67 drugs
    68 effect
    69 epistasis networks
    70 epistatic effects
    71 epistatic interactions
    72 evidence
    73 factors
    74 framework
    75 function prediction
    76 gene modules
    77 gene networks
    78 gene-disease associations
    79 gene-gene interaction networks
    80 genes
    81 genetic effects
    82 genetic risk factors
    83 genetic variants
    84 genome-wide association studies
    85 genome-wide association study dataset
    86 genotype information
    87 heavy computational cost
    88 hypersensitivity
    89 information
    90 information-theoretic measures
    91 integrated network
    92 interaction
    93 interaction networks
    94 investigation
    95 knowledgebase
    96 measures
    97 mechanism
    98 medical conditions
    99 method
    100 module
    101 multiple genetic variants
    102 multiple single nucleotide polymorphisms
    103 nasal polyposis
    104 network
    105 network analysis
    106 non-steroidal anti-inflammatory drugs
    107 nucleotide polymorphisms
    108 number
    109 part
    110 polymorphism
    111 polyposis
    112 population
    113 portal
    114 prediction
    115 previous studies
    116 properties
    117 respiratory disease
    118 results
    119 risk factors
    120 significance
    121 single nucleotide polymorphisms
    122 small number
    123 statistical analysis
    124 study
    125 study dataset
    126 susceptibility
    127 theoretic measures
    128 thorough investigation
    129 time
    130 topological properties
    131 treatment
    132 underlying biological mechanisms
    133 variants
    134 schema:name Integrative information theoretic network analysis for genome-wide association study of aspirin exacerbated respiratory disease in Korean population
    135 schema:pagination 31
    136 schema:productId N2c85de50202a411399ce6ea9f303ce68
    137 N86caa882074e42f2be4531c8df5bff8d
    138 Nee9e5c6d47264d2c8c274e1619b1b74a
    139 schema:sameAs https://app.dimensions.ai/details/publication/pub.1085588852
    140 https://doi.org/10.1186/s12920-017-0266-1
    141 schema:sdDatePublished 2022-05-10T10:15
    142 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    143 schema:sdPublisher N2de3555d7ef441c983ece35c5ce430ce
    144 schema:url https://doi.org/10.1186/s12920-017-0266-1
    145 sgo:license sg:explorer/license/
    146 sgo:sdDataset articles
    147 rdf:type schema:ScholarlyArticle
    148 N0ffc99a760e44838b1148913c968f290 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    149 schema:name Asthma, Aspirin-Induced
    150 rdf:type schema:DefinedTerm
    151 N2c85de50202a411399ce6ea9f303ce68 schema:name doi
    152 schema:value 10.1186/s12920-017-0266-1
    153 rdf:type schema:PropertyValue
    154 N2de3555d7ef441c983ece35c5ce430ce schema:name Springer Nature - SN SciGraph project
    155 rdf:type schema:Organization
    156 N37aac2530dbb4155b25b79433c3b2f6a schema:volumeNumber 10
    157 rdf:type schema:PublicationVolume
    158 N37d0f0bb3420498592a8684cd9d59e20 schema:issueNumber Suppl 1
    159 rdf:type schema:PublicationIssue
    160 N3a15e098ed744efbb0d67099f9127df1 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    161 schema:name Genome-Wide Association Study
    162 rdf:type schema:DefinedTerm
    163 N3a1a8df914c74b58a38292b40b83b75d rdf:first sg:person.010200047735.02
    164 rdf:rest N4b5afe9864894fdd8ecbd7a4e57569c8
    165 N4b5afe9864894fdd8ecbd7a4e57569c8 rdf:first sg:person.01255615162.64
    166 rdf:rest N893fd48cf2e24fab9725f4d0d23f90dc
    167 N4d1fc1d071b5467d97915b8a72ce2bb2 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    168 schema:name Epigenesis, Genetic
    169 rdf:type schema:DefinedTerm
    170 N679dab8d00e34e2b9ee63b3b8cfe404b rdf:first sg:person.0745210405.35
    171 rdf:rest N3a1a8df914c74b58a38292b40b83b75d
    172 N6bd5e09f7ed547149ea3e28c24c647fb schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    173 schema:name Republic of Korea
    174 rdf:type schema:DefinedTerm
    175 N6e02a263c05547d39c37145e057b932c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    176 schema:name Humans
    177 rdf:type schema:DefinedTerm
    178 N86caa882074e42f2be4531c8df5bff8d schema:name pubmed_id
    179 schema:value 28589859
    180 rdf:type schema:PropertyValue
    181 N89284011f1d440ecb1ae1a9de5bc0a05 rdf:first sg:person.011037520407.10
    182 rdf:rest Ned281ca45d704073b651c28fbd005b80
    183 N893fd48cf2e24fab9725f4d0d23f90dc rdf:first sg:person.01147724375.97
    184 rdf:rest rdf:nil
    185 Nb378dbd9658448a6b8012e9472ce8f68 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    186 schema:name Polymorphism, Single Nucleotide
    187 rdf:type schema:DefinedTerm
    188 Ncef87b20e0ac45739aadd7883b850f7a schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    189 schema:name Gene Ontology
    190 rdf:type schema:DefinedTerm
    191 Ned281ca45d704073b651c28fbd005b80 rdf:first sg:person.0741347305.11
    192 rdf:rest Nf65fcf94c850483e85e3c23b3ffeec17
    193 Nee9e5c6d47264d2c8c274e1619b1b74a schema:name dimensions_id
    194 schema:value pub.1085588852
    195 rdf:type schema:PropertyValue
    196 Nf43b0ded07b74bd8affcb479d42caf54 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    197 schema:name Gene Regulatory Networks
    198 rdf:type schema:DefinedTerm
    199 Nf65fcf94c850483e85e3c23b3ffeec17 rdf:first sg:person.01341553516.04
    200 rdf:rest N679dab8d00e34e2b9ee63b3b8cfe404b
    201 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    202 schema:name Biological Sciences
    203 rdf:type schema:DefinedTerm
    204 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
    205 schema:name Genetics
    206 rdf:type schema:DefinedTerm
    207 sg:journal.1039191 schema:issn 1755-8794
    208 schema:name BMC Medical Genomics
    209 schema:publisher Springer Nature
    210 rdf:type schema:Periodical
    211 sg:person.010200047735.02 schema:affiliation grid-institutes:grid.251916.8
    212 schema:familyName Park
    213 schema:givenName Hae-Sim
    214 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.010200047735.02
    215 rdf:type schema:Person
    216 sg:person.011037520407.10 schema:affiliation grid-institutes:grid.251916.8
    217 schema:familyName Wang
    218 schema:givenName Sehee
    219 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011037520407.10
    220 rdf:type schema:Person
    221 sg:person.01147724375.97 schema:affiliation grid-institutes:grid.251916.8
    222 schema:familyName Sohn
    223 schema:givenName Kyung-Ah
    224 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01147724375.97
    225 rdf:type schema:Person
    226 sg:person.01255615162.64 schema:affiliation grid-institutes:grid.411261.1
    227 schema:familyName Kim
    228 schema:givenName Seung-Hyun
    229 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01255615162.64
    230 rdf:type schema:Person
    231 sg:person.01341553516.04 schema:affiliation grid-institutes:grid.29857.31
    232 schema:familyName Kim
    233 schema:givenName Dokyoon
    234 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01341553516.04
    235 rdf:type schema:Person
    236 sg:person.0741347305.11 schema:affiliation grid-institutes:grid.39382.33
    237 schema:familyName Jeong
    238 schema:givenName Hyun-hwan
    239 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0741347305.11
    240 rdf:type schema:Person
    241 sg:person.0745210405.35 schema:affiliation grid-institutes:grid.251916.8
    242 schema:familyName Wee
    243 schema:givenName Kyubum
    244 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0745210405.35
    245 rdf:type schema:Person
    246 sg:pub.10.1007/978-3-540-39804-2_22 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029899008
    247 https://doi.org/10.1007/978-3-540-39804-2_22
    248 rdf:type schema:CreativeWork
    249 sg:pub.10.1007/s00438-012-0685-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1048639933
    250 https://doi.org/10.1007/s00438-012-0685-9
    251 rdf:type schema:CreativeWork
    252 sg:pub.10.1007/s00439-012-1247-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040692595
    253 https://doi.org/10.1007/s00439-012-1247-2
    254 rdf:type schema:CreativeWork
    255 sg:pub.10.1007/s10875-008-9190-7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043854554
    256 https://doi.org/10.1007/s10875-008-9190-7
    257 rdf:type schema:CreativeWork
    258 sg:pub.10.1038/gene.2010.37 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020223793
    259 https://doi.org/10.1038/gene.2010.37
    260 rdf:type schema:CreativeWork
    261 sg:pub.10.1038/ng2110 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008850890
    262 https://doi.org/10.1038/ng2110
    263 rdf:type schema:CreativeWork
    264 sg:pub.10.1038/nri3519 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010662448
    265 https://doi.org/10.1038/nri3519
    266 rdf:type schema:CreativeWork
    267 sg:pub.10.1186/1471-2105-12-364 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034115657
    268 https://doi.org/10.1186/1471-2105-12-364
    269 rdf:type schema:CreativeWork
    270 sg:pub.10.1186/1471-2105-15-1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030123122
    271 https://doi.org/10.1186/1471-2105-15-1
    272 rdf:type schema:CreativeWork
    273 sg:pub.10.1186/1471-2105-15-102 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045340124
    274 https://doi.org/10.1186/1471-2105-15-102
    275 rdf:type schema:CreativeWork
    276 sg:pub.10.1186/s13040-014-0034-0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043371184
    277 https://doi.org/10.1186/s13040-014-0034-0
    278 rdf:type schema:CreativeWork
    279 sg:pub.10.1186/s13040-015-0077-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1034836750
    280 https://doi.org/10.1186/s13040-015-0077-x
    281 rdf:type schema:CreativeWork
    282 sg:pub.10.1186/s13048-015-0124-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024213499
    283 https://doi.org/10.1186/s13048-015-0124-8
    284 rdf:type schema:CreativeWork
    285 sg:pub.10.1186/s13048-015-0171-1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045835208
    286 https://doi.org/10.1186/s13048-015-0171-1
    287 rdf:type schema:CreativeWork
    288 sg:pub.10.1385/criai:24:2:169 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047553932
    289 https://doi.org/10.1385/criai:24:2:169
    290 rdf:type schema:CreativeWork
    291 grid-institutes:grid.251916.8 schema:alternateName Department of Allergy and Clinical Immunology, Ajou University School of Medicine, Suwon, South Korea
    292 Department of Software and Computer Engineering, Ajou University, 16499, Suwon, South Korea
    293 schema:name Department of Allergy and Clinical Immunology, Ajou University School of Medicine, Suwon, South Korea
    294 Department of Software and Computer Engineering, Ajou University, 16499, Suwon, South Korea
    295 rdf:type schema:Organization
    296 grid-institutes:grid.29857.31 schema:alternateName The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
    297 schema:name Department of Biomedical & Translational Informatics, Geisinger Health System, 17822, Danville, PA, USA
    298 The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
    299 rdf:type schema:Organization
    300 grid-institutes:grid.39382.33 schema:alternateName Department of Human and Molecular Genetics, Baylor College of Medicine, 77030, Houston, Texas, USA
    301 schema:name Department of Human and Molecular Genetics, Baylor College of Medicine, 77030, Houston, Texas, USA
    302 Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, 77030, Houston, Texas, USA
    303 rdf:type schema:Organization
    304 grid-institutes:grid.411261.1 schema:alternateName Translational Research Laboratory for Inflammatory Disease, Clinical Trial Center, Ajou University Medical Center, Suwon, South Korea
    305 schema:name Department of Allergy and Clinical Immunology, Ajou University School of Medicine, Suwon, South Korea
    306 Translational Research Laboratory for Inflammatory Disease, Clinical Trial Center, Ajou University Medical Center, Suwon, South Korea
    307 rdf:type schema:Organization
     




    Preview window. Press ESC to close (or click here)


    ...